A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi
ABSTRACT Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, t...
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| Format: | Article |
| Language: | English |
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Wiley
2025-01-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.70798 |
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| author | Holly V. Nelson Arthur Georges Katherine A. Farquharson Elspeth A. McLennan Jane L. DeGabriel Katherine Belov Carolyn J. Hogg |
| author_facet | Holly V. Nelson Arthur Georges Katherine A. Farquharson Elspeth A. McLennan Jane L. DeGabriel Katherine Belov Carolyn J. Hogg |
| author_sort | Holly V. Nelson |
| collection | DOAJ |
| description | ABSTRACT Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger‐sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152‐base‐pair‐long fragment of the cytochrome oxidase 1 (CO1) gene and a 186‐base‐pair‐long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ. |
| format | Article |
| id | doaj-art-88cf102ccf614828b7aed2ace993f25d |
| institution | Kabale University |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj-art-88cf102ccf614828b7aed2ace993f25d2025-01-29T05:08:41ZengWileyEcology and Evolution2045-77582025-01-01151n/an/a10.1002/ece3.70798A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesiHolly V. Nelson0Arthur Georges1Katherine A. Farquharson2Elspeth A. McLennan3Jane L. DeGabriel4Katherine Belov5Carolyn J. Hogg6School of Life and Environmental Sciences The University of Sydney Sydney New South Wales AustraliaInstitute for Applied Ecology University of Canberra Bruce Australian Capital Territory AustraliaSchool of Life and Environmental Sciences The University of Sydney Sydney New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Sydney New South Wales AustraliaNSW Department of Climate Change, The Environment, Energy and Water Parramatta New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Sydney New South Wales AustraliaSchool of Life and Environmental Sciences The University of Sydney Sydney New South Wales AustraliaABSTRACT Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger‐sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152‐base‐pair‐long fragment of the cytochrome oxidase 1 (CO1) gene and a 186‐base‐pair‐long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.https://doi.org/10.1002/ece3.70798Bellinger River turtleeDNAgenomic dataMyuchelys georgesireference genome |
| spellingShingle | Holly V. Nelson Arthur Georges Katherine A. Farquharson Elspeth A. McLennan Jane L. DeGabriel Katherine Belov Carolyn J. Hogg A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi Ecology and Evolution Bellinger River turtle eDNA genomic data Myuchelys georgesi reference genome |
| title | A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi |
| title_full | A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi |
| title_fullStr | A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi |
| title_full_unstemmed | A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi |
| title_short | A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi |
| title_sort | genomic based workflow for edna assay development for a critically endangered turtle myuchelys georgesi |
| topic | Bellinger River turtle eDNA genomic data Myuchelys georgesi reference genome |
| url | https://doi.org/10.1002/ece3.70798 |
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